American Journal of Medical Genetics Part A

Genetic variants in the gene Ankyrin Repeat Domain 11 (ANKRD11) and deletions in 16q24.3 are known to cause KBG syndrome, a rare syndrome associated with craniofacial, intellectual, and neurobehavioral anomalies. We report 25 unpublished individuals from 22 families, all with molecularly confirmed diagnoses of KBG syndrome. Twenty-one individuals have de novo variants, three have inherited variants, and one is inherited from a parent exhibiting low-level mosaicism. Of the variants, 20 are truncating (frameshift or nonsense), and the remaining five individuals have missense variants (with one of these in three family members). One of the missense variants has been found in at least two other affected individuals. We created a novel protocol for collection and reporting of data, including prospectively interviewing these individuals and their families throughout eight countries via videoconferencing by a single clinician. Participants medical records, including imaging, were reviewed, and data was uploaded to the Human Disease Gene website using Human Phenotype Ontology (HPO) terms. Photos of the participants were submitted to GestaltMatcher and Face2Gene (FDNA Inc, USA) for facial analysis, and we found similar facial phenotypes among the participants. Within our cohort, common traits included short stature, macrodontia, anteverted nares, wide nasal bridge, wide nasal base, thick eyebrows, synophrys and hypertelorism. Seventy-two percent of participants had gastrointestinal complaints and 80% had hearing loss. Three participants were started on growth hormone with positive results. Behavioral issues and global developmental delays were found in most participants. Neurologic abnormalities including seizures and/or EEG abnormalities were also very common (44%), suggesting that early detection and seizure prophylaxis could be an important point of intervention. Twenty-four percent were diagnosed with attention deficit hyperactivity disorder (ADHD) and 28% were diagnosed with autism spectrum disorder (ASD). Additionally, we have identified minimally reported symptoms, including recurrent sinus infections (16%) and previously unreported migraines (20%). Based on the videoconferencing and these data, we provide a set of recommendations regarding diagnostic and treatment approaches for KBG syndrome.

ObjectiveWolfram syndrome (WFS) is an autosomal recessive disorder associated with juvenile-onset diabetes mellitus, optic atrophy, diabetes insipidus, and sensorineural hearing loss. We sought to elucidate the relationship between genotypic and phenotypic presentations of Wolfram syndrome which would assist clinicians in classifying the severity and prognosis of Wolfram syndrome more accurately. ApproachPatient data from the Washington University International Registry and Clinical Study for Wolfram Syndrome and patient case reports were analyzed to select for patients with two recessive mutations in the WFS1 gene. Mutations were classified as being either nonsense/frameshift variants or missense/in-frame insertion/deletion variants and statistical analysis was performed using unpaired and paired t-tests and one- and two-way ANOVA with Tukeys or Dunnetts tests. ResultsA greater number of genotype variants correlated with earlier onset and a more severe presentation of Wolfram syndrome. Secondly, non-sense and frameshift variants had more severe phenotypic presentations than missense variants, as evidenced by optic atrophy emerging significantly earlier in patients with 2 nonsense/frameshift alleles compared with 0 missense transmembrane variants. In addition, the number of transmembrane in-frame variants demonstrated a statistically significant dose-effect on age of onset of diabetes mellitus and optic atrophy. Summary / ConclusionsThe results contribute to our current understanding of the genotype-phenotype relationship of Wolfram syndrome, suggesting that alterations in coding sequences result in significant changes in the presentation and severity of Wolfram. The impact of these findings is significant, as the results will aid clinicians in predicting more accurate prognoses and pave the way for personalized treatments for Wolfram syndrome.

BackgroundApproximately 30-40% of genetic and rare disorders manifest with distinct facial patterns. Traditionally, clinical geneticists have qualitatively assessed facial morphology to support preliminary diagnosis and guide confirmatory genetic testing. However, enhancing early diagnostic accuracy through facial biomarkers demands advanced 3D technologies for analyzing facial dysmorphologies, a deeper understanding of condition-specific disruptions in facial development, and a broader inclusion of diverse human populations. To bridge this gap, we analyzed the 3D phenotypes associated with four genetic syndromes in an admixed Latin American population from Colombia. The sample comprised 47 individuals diagnosed with Down (DS), Morquio (MS), Noonan (NS), and Neurofibromatosis type 1 (NF1) syndromes along with 49 controls within the same age range. For each participant, we generated a 3D facial model using a multi-camera photogrammetric system and registered the 3D coordinates of 21 anatomical facial landmarks. Geometric morphometrics methods were employed to characterize syndrome-specific 3D facial dysmorphologies and to assess their variation compared to controls. We also examined whether these syndromes alter the ontogenetic trajectory of facial growth. ResultsFacial shape differed significantly in all syndromes except NF1. Consistently with previous 2D studies, we identified population-specific facial features in Colombian patients that are not reported in individuals of European descent. Pooled 3D analyses revealed a continuous spectrum of facial dysmorphology, with MS displaying the most distinct morphology and an altered ontogenic pattern. Facial size, sex and age were all significant factors modulating facial shape, with diagnosis explaining 14% of variation in facial morphology. ConclusionsOverall, these findings highlight the importance of accounting for interpopulation, sex and ontogenic variation in facial phenotypes to improve the diagnostic utility and of facial biomarkers. Such approaches may contribute to shortening the diagnostic odyssey for individuals with syndromic and rare genetic conditions.

ObjectiveTo identify rare and common CNVs associated with strabismus and amblyopia and to determine whether these variants reveal overlapping genetic mechanisms between the two disorders. DesignCase-control association study using structural variant calls from short-read whole- genome sequencing. Subject, participants and controls1,141 adults with strabismus, 566 with amblyopia (157 with both), and controls (95,806 for strabismus; 96,381 for amblyopia) enrolled in the All of Us Research Program and with available structural variant calls. MethodsCNVs were called using the GATK-SV pipeline from short-read whole genome sequencing (srWGS). After instituting a variety of quality control measures, including requiring two types of evidence and being identified by two different calling algorithms, CNVs present in 20 or more affected individuals were divided into rare (<1% population frequency) and common (>1% population frequency). The rates of each CNV were compared between affected individuals and controls. Significant CNVs were manually verified in IGV. Functional effects were annotated using Varient Effect Predictor from Ensembl. Main Outcome MeasuresOdds ratios for CNV carrier status in cases versus controls, adjusted for multiple testing (Benjamini-Hochberg FDR < 0.05); functional annotation, dosage sensitivity, regulatory element overlap, and pathway enrichment. ResultsFourteen rare and 29 common CNVs were significantly associated with strabismus; 1 rare and 2 common CNVs were associated with amblyopia (45 unique CNVs total). The rare CNV associated with amblyopia is an intronic deletion in MDGA2. Two common intronic deletions (GRIN2B; CACNA1B) were associated with both conditions and highly predictive of comorbid strabismus and amblyopia (47% comorbidity when both present, p < .001). Implicated genes predominantly affect synapse formation and function (e.g., CSMD1, GRIN2B, CACNA1B, RIMS1), neuronal migration (e.g., TUBB, EML1), and neurodevelopment; 64% have known neurodevelopmental phenotypes and 27% have been linked to mental health disorders. ConclusionsCNVs highlight synaptic and neurodevelopmental pathways as central to strabismus and amblyopia etiology and provide the first evidence of shared genetic risk. The combination of GRIN2B and CACNA1B deletions identify strabismus patients at high risk for amblyopia.

BackgroundFacioscapulohumeral dystrophy (FSHD) is typically caused by contraction of the D4Z4 repeat array at chromosome 4q35 (FSHD1) or pathogenic variants in the SMCHD1 gene (FSHD2). While these account for the majority of cases, 1-2% of patients present with clinical features of FSHD but lack a known genetic cause, revealing a diagnostic gap. In Previous studies, we identified over 70 patients with structural rearrangements involving the 4q35 or 10q26 loci, some of which may be pathogenic in the absence of other FSHD-associated features. MethodsGiven their diagnostic relevance, we performed detailed structural analyses of these rearrangements using high-resolution long-read sequencing technologies (Oxford Nanopore and PacBio) for seven patients carrying different structural variants of the 4q35 or 10q26 loci. ResultsThese approaches enabled us to resolve nucleotide-level architecture and methylation patterns across the 4q35 and 10q26 loci. We show that duplicated alleles arise from intrachromosomal recombination between LSau and {beta}-satellite elements, producing variable deletions within D4Z4, with breakpoints differing among patients. These complex structural variants are not detectable using standard technologies like Bionano Optical Genome Mapping and require manual curation for identification. Importantly, determining the pathogenic relevance of these rearrangements necessitates integrating structural and epigenetic features typically associated with FSHD. ConclusionThe results highlight the importance of thorough molecular analysis for FSHD patients who test negative for FSHD1 and FSHD2, advocating for expanded diagnostic strategies. Comprehensive evaluation of 4q35 structural variants is essential for improving diagnosis accuracy, guiding genetic counseling, and optimizing care for patients with atypical FSHD presentations. Graphical AbstractHypothetical model for the formation of 4q35 intrachromosomal duplications. We speculate that the breakpoint occurs in the proximal region of a D4Z4 units that corresponds to LSau repeats and involves the distal {beta}satellite array. The duplicated array is then inserted in the distal part of the locus mapped by the most telomeric red probe used for MC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/25333030v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@10edaf3org.highwire.dtl.DTLVardef@48bd67org.highwire.dtl.DTLVardef@18add58org.highwire.dtl.DTLVardef@1c9c14c_HPS_FORMAT_FIGEXP M_FIG C_FIG

OBJECTIVEVan der Woude Syndrome (VWS) classically presents with combinations of lip pits (LP) and orofacial clefts, with marked phenotypic discordance even amongst individuals carrying the same mutation. Such discordance suggests a possible role for epigenetic factors as phenotypic modifiers. Both IRF6, causal for 70% of VWS cases, and TP63 interact in a regulatory loop to coordinate epithelial proliferation and differentiation for palatogenesis. We hypothesize that differential DNA methylation (DNAm) in CpG sites within regulatory regions of IRF6 and TP63 are associated with VWS phenotypic discordance. METHODSWe measured DNAm levels of CpG sites located in the promoter regions of IRF6 and TP63 and in an IRF6 enhancer element (MCS9.7) in 83 individuals with VWS grouped within 5 phenotypes for primary analysis: 1=CL+/-P+LP, 2=CL+/-P, 3=CP+LP, 4=CP, 5=LP and 2 phenotypes for secondary analysis: 1=any cleft and LP, 2= any cleft without LP. DNA samples were bisulfite converted and pyrosequenced with target-specific primers. Methylation levels were compared amongst phenotypes. RESULTSCpG sites in the IRF6 promoter showed statistically significant differences in methylation among phenotypic groups in both analyses (P<0.05). Individuals with any form of cleft (Groups 1-4) had significantly higher methylation levels than individuals with lip pits only (Group 5). In the secondary analysis, individuals in Group 1 (cleft+LP) had significantly higher methylation than Group 2 (cleft only). CONCLUSIONResults indicated that hypermethylation of the IRF6 promoter is associated with more severe phenotypes (any cleft +/- lip pits); thus, possibly impacting an already genetically weakened IRF6 protein and leading to a more severe phenotype.

The study of Intersex traits or Differences of Sex Development (I/DSD) is an imperative area within medical genetics that confronts a long-standing problem: the prevalence of these conditions in the population is not fully clear, likely undercounted, and therefore no universally agreed upon numbers exist. Proportions among rare differences are not fully understood. While each specific I/DSD condition is individually rare, together they are estimated to affect about 0.7-1.7% of people worldwide (Fausto-Sterling, 1993). Over 10% of individuals with I/DSD traits exhibit comorbidities affecting other bodily systems, suggesting a broader, systemic impact of these conditions. The comprehensive phenotypic spectrum and systemic implications of I/DSD traits are not well-documented, likely due to social, cultural, and privacy concerns that may contribute to the under-phenotyping of genital variations. This research aims to delineate the disease landscape associated with I/DSD traits. By using the Online Mendelian Inherit ance in Man (OMIM) database, a comprehensive resource for human genes and genetic disorders, we compiled an expert list of 155 Human Phenotype Ontology (HPO) terms that encompass the entirety of the medically defined I/DSD space. These terms were cross-referenced with the OMIM database to pinpoint diseases annotated with these HPO terms. Out of 8,181 phenotypically detailed diseases listed in OMIM and included in the HPO database, we discovered that 1,264 (15.5%) have associations with I/DSD-related HPO terms, signifying their presence in I/DSD traits. This substantial overlap underscores the need to rethink I/DSD not just as isolated anomalies but as a continuum of conditions that are crucial for a broader understanding of health issues. It also highlights that I/DSD traits are relatively common within the realm of rare differences, emphasizing the necessity for specialists, such as clinical geneticists, to be well-versed in I/DSD. Our findings call for a shift in the medical communitys perception and approach to studying I/DSD traits. Further research is required to confirm these associations and to explore the relationship between I/DSD traits and overall health.

Background and ObjectivesStrabismus, a misalignment of the eyes, is an important risk factor for amblyopia and visual impairment in the pediatric population. Several studies have reported an increased likelihood of strabismus in persons on the autism spectrum, but prevalence estimates in this group vary greatly. MethodsWe searched multiple databases to identify peer-reviewed articles published in English through November 1, 2020 that provided estimates of strabismus prevalence in autistic individuals. Prevalence estimates were synthesized using Bayesian random-effects meta-analysis, and sensitivity analysis was also performed using only the subset of studies that recruited participants from non-ophthalmologic settings and identified strabismus using structured ocular exams. Bayesian meta-regression was used to assess potential moderators of prevalence across studies. ResultsA total of 151 nonduplicate articles were screened, of which 22 were included in the meta-analysis (k=28 samples, nAUT=113,227). The meta-analytic point prevalence of strabismus in autistic individuals was 13.4% (95% CrI [8.3,19.4]), and sensitivity analysis produced a very similar estimate (14.0% [7.0,22.0], nAUT=581). Esotropia was the predominant subtype of strabismus reported, accounting for approximately 55% of cases. Reported prevalence rates were higher in younger samples (BF10=13.43, R2Het =0.273) and samples recruited from optometry/ophthalmology clinics (BF10=11.47, R2Het =0.238). ConclusionThis meta-analysis found a high prevalence of strabismus in autistic individuals, with rates 3-10 times that of the general population. As untreated strabismus is a major risk factor for amblyopia in young children, these findings underscore the importance of timely screening and assessment of ocular problems in persons on the autism spectrum. Whats Known on This SubjectStrabismus has been reported to be more prevalent in individuals on the autism spectrum, but estimates have been very imprecise, ranging from 3-84% across studies. What This Study AddsThis study performs the first quantitative synthesis of strabismus prevalence in over 100,000 autistic individuals, generating more precise estimates of the prevalence of strabismus in the autistic population. Factors contributing to the large differences between studies are also examined using meta-regression.

BackgroundDisturbances in the intricate processes that control craniofacial morphogenesis can result in birth defects, most common of which are orofacial clefts (OFCs). Nonsyndromic cleft lip (nsCL), one of the phenotypic forms amongst OFCs, has a non-random laterality presentation with the left side being affected twice as often compared to the right side. This study investigates the etiology of nsCL and the factors contributing to its laterality using a pair of monozygotic twins with mirror-image cleft lip. MethodsWe conducted whole-genome sequencing (WGS) analyses in a female twin pair with mirror image nsCL, their affected mother and unaffected father to identify etiopathogenic variants. Additionally, to identify possible cleft lip laterality modifiers, DNA-methylome analysis was conducted to test for differential methylation patterns between the mirror twins. Lastly, DNA methylation patterns were also analyzed on an independent cohort of female cases with unilateral cleft lip (left=22; right=17) for replication purposes. ResultsWe identified a protein-altering variant in FGF20 (p.Ile79Val) within the fibroblast growth factor interacting family domain segregating with the nsCL in this family. Concurrently, DNA-methylome analysis identified differential methylation regions (DMRs) upstream of Zinc-finger transcription factor ZFP57 ({Delta}{beta} > 5%). Replication of these results on an independent cohort, confirmed these DMRs, emphasizing their biological significance (p<0.05). Enrichment analysis indicated that these DMRs are involved in DNA methylation during early embryo development (FDR adjusted p-value = 1.3241E-13). Further bioinformatics analyses showed one of these DMRs acting as a binding site for transcription factor AP2A (TFAP2A), a key player in craniofacial development. Interactome analysis also suggested a potential role for ZFP57 in left/right axis specification, thus emphasizing its significance in cleft laterality. ConclusionThis study provides novel insights into the etiology of nsCL and its laterality, suggesting an interplay between etiopathogenic variants and DNA methylation in cleft laterality. Our findings elucidate the intricate mechanisms underlying OFCs development. Understanding these factors may offer new tools for prevention and management of OFCs, alleviating the burden on affected individuals, their families and global health.

BackgroundStrabismus is a complex oculomotor condition characterized by a misalignment of the visual axis. The genetics of strabismus are poorly defined although a few candidate genes have been identified, among which is the WNT2 gene. Our study was designed to assess the association of single nucleotide polymorphisms (SNPs) of WNT2 in Pakistani strabismus patients. MethodsA total of six SNPs, three intronic and three in the 3 untranslated region, were screened in the current study. Logistic regression was performed using a dominant, recessive and additive model to determine the association of SNPs with strabismus and its clinical subtypes: esotropia and exotropia. Furthermore, haplotype analysis was performed. ResultsRegression analysis revealed an association of rs2896218, rs3779550, rs2285544 and rs4730775 with strabismus under the dominant model. When analyzed separately, rs2896218 and rs2285544 were found to be associated with both esotropia and exotropia, while rs4730775 was significantly associated only with exotropia under the dominant model. Based on clinical parameters, rs2896218, rs2285544 and rs4730775 were also found to be associated with the group of strabismus patients who were diagnosed at birth, but not in the group of patients who were diagnosed later in life. Haplotype analysis revealed that the haplotype A T T (corresponding to rs2896218, rs3779550 and rs2285544) was significantly more prevalent in the strabismus group. ConclusionOverall, the results of the present study suggests an association of WNT2 polymorphisms with strabismus and its subtypes in the Pakistani population, though further studies are needed to elucidate their role in strabismus etiology. What is already known on this topic O_LIStrabismus is a common oculomotor condition with a genetic component. C_LIO_LIWNT2 has been identified as a candidate gene for comitant strabismus. C_LI What this study adds O_LITwo WNT2 polymorphisms not previously reported have been found to be associated with strabismus. C_LIO_LIThere are genetic variations between clinical subtypes of strabismus (esotropia and exotropia). C_LIO_LIWNT2 polymorphisms are associated with age at the time of diagnosis and family history. C_LIO_LICombinations of different alleles (haplotypes) are associated with the disease. C_LI How this study might affect research, practice or policy O_LIOur study adds to the limited genetic data for strabismus and suggests further studies on the role of WNT2 in strabismus causation. C_LI

Our study of 61 children with Ogden Syndrome, an X-linked disorder due to NAA10 gene mutations, demonstrated a high prevalence of growth failure, with weight and height percentiles often in the failure-to-thrive diagnostic range; although dramatic weight fluctuations and phenotypic variability is evidenced in the growth parameters of this population. Although never previously explored in depth, the gastrointestinal pathology associated with OS includes feeding difficulties in infancy, dysphagia, GERD/silent reflux, vomiting, constipation, diarrhea, bowel incontinence, and presence of eosinophils on esophageal endoscopy, in order from most to least prevalent. Additionally, the gastrointestinal symptom profile for children with this syndrome has been expanded to include eosinophilic esophagitis, cyclic vomiting syndrome, Mallory Weiss tears, abdominal migraine, esophageal dilation, and subglottic stenosis. Although the exact cause of poor growth in OS probands is unclear and the degree of contribution to this problem by GI symptomatology remains uncertain, an analysis including nine G-tube or GJ-tube fed probands demonstrates that G/GJ-tubes are overall efficacious with respect to improvements in weight gain and caregiving. The choice to insert a gastrostomy or gastrojejunal tube to aid with weight gain is often a challenging decision to make for parents, who may alternatively choose to rely on oral feeding, caloric supplementation, calorie tracking, and feeding therapy. In this case, if OS children are not tracking above the FTT range past 1 year of age despite such efforts, they should promptly undergo G-tube placement to avoid prolonged growth failure. If G-tubes are not immediately inducing weight gain after insertion, recommendations include altering formula, increasing caloric input, or exchanging a G-tube for a GJ-tube by means of a minimally invasive procedure. Future directions could include a prospective natural history study investigating whether G/GJ tube insertion affects the cognitive trajectory, rate of reaching developmental milestones, and GI symptomatology of OS children in a positive or negative manner.

CTNNB1 syndrome is a rare neurodevelopmental disorder caused by pathogenic variants in the CTNNB1 gene. Although its core clinical manifestations have been increasingly recognised, longitudinal data on cognitive, behavioural and motor trajectories remain limited, and the craniofacial phenotype has not previously been quantitatively characterised. This study provides longitudinal evidence on the cognitive, clinical and psychological profile of individuals with CTNNB1 syndrome, together with a detailed three-dimensional morphometric analysis of facial morphology. Cognitive, clinical, psychological and neuropsychological data were collected at two time points (T0 and T1), separated by a one-year interval, using a comprehensive and standardised assessment protocol. Longitudinal analyses indicated stability across most domains, with no evidence of systematic regression. A significant improvement in gross motor functioning was observed, particularly among younger participants. Linear mixed-effects models showed that age moderated developmental change, with younger individuals exhibiting greater gains over time in gross motor skills and adaptive behaviour compared to older participants. Three-dimensional facial morphometric analyses revealed a distinctive and statistically significant craniofacial pattern associated with CTNNB1 syndrome, independent of age and facial size. This phenotype was characterised by midfacial narrowing, reduced midface projection and mandibular retrusion. Importantly, facial shape variation was significantly associated with externalising behavioural problems and clinically relevant behavioural difficulties, suggesting a link between craniofacial morphology and behavioural severity. This study represents the first integrated longitudinal characterisation of CTNNB1 syndrome combining neurodevelopmental follow-up with quantitative craniofacial phenotyping. The findings indicate slow but progressive improvement in specific clinical domains during childhood and adolescence, alongside relative stability in global adaptive functioning, and highlight three-dimensional facial morphology as a sensitive structural biomarker for phenotypic stratification and clinical monitoring in CTNNB1 syndrome. Lay summaryThis study is the first to describe how children with CTNNB1 syndrome, a rare genetic condition that leads to global developmental delays, develop over time. We also performed advanced facial analysis to look for common facial features among patients.

BackgroundHypospadias is a congenital disorder of male genital formation where the urinary opening is not on the head of the penis and genetic factors play an important role in the incidence of this early developmental defect in 46,XY individuals, in both isolated and syndromic forms. Children born small for gestational age (SGA) present a high frequency of hypospadias of undetermined etiology, ranging from 15 to 30%, but the detection of hypospadias etiology remains low.\n\nPatients and methodsfrom a cohort of 46,XY DSD patients, we identified 25 SGA children with medium or proximal hypospadias; four of them with associated syndromic characteristics. DNA samples from subjects were studied by massively parallel targeted sequencing (MPTS) using a targeted panel. MLPA was used for molecular diagnosis in two children with clinical phenotype of Silver Russel syndrome.\n\nResultsLoss of DNA methylation (11p15 LOM) at ICR1 was identified in two out of four syndromic children. The other syndromic patient had 3M syndrome phenotype and two novel likely-pathogenic variants in compound heterozygous state were found in CUL7 gene. The last syndromic subject had Mulibrey nanism and, a homozygous variant in TRIM37 was identified in the patient and confirmed in heterozygous state in the mother. Among non-syndromic children seven rare heterozygous variants with uncertain significance in six DSD-related genes were identified: two children had DHX37 variants associated with GATA4 and WWOX variants, respectively; three children had heterozygous variants, in WT1, IGF1R, and BMP8B genes.\n\nConclusionPathogenic or likely-pathogenic variants in DSD-related genes were not identified in non-syndromic SGA children with hypospadias, suggesting that multi-factorial causes, unknown genes or unidentified environmental factors (epigenetic defects), may be involved in the etiology of this condition.

PurposeFragile X syndrome (FXS) is a hereditary genetic condition, caused by the expansion of the trinucleotide CGG repeated over 200 times (full mutation) in the 5UTR (untranslated region) regulatory region of the FMR1 gene, which leads to the absence of FMRP protein. Although the clinical standard genetic confirmation for FXS diagnosis is limited to the repeats, the use of gene sequencing techniques allowed the identification of genetic variants that occur throughout the entire FMR1 gene, including protein-coding and 3UTR gene regions. These mutations may also cause the inactivation of FMR1 gene, leading to the FXS phenotypes in individuals with CGG repeat expansions at a normal level (5-44 repeats) or at the premutation level (between 55 and 200 repeats), and not necessarily diagnosed with FXS. MethodsTo investigate how widespread the genetic mutations occurring throughout the FMR1 gene locus are, we performed a Systematic Literature Review (SLR) to identify and synthesize a catalog of disease-causing mutations in the gene that are related to cause FXS or correlated conditions. ResultsAfter a detailed literature analysis, we found 44 single nucleotide variants (SNV) at the locus of the FMR1 gene associated with developmental delay and/or intellectual disability, also including characteristics of FXS. Deletions involving the FMR1 gene that remove several other genes were also found to be associated with FXS phenotype and ovarian problems, besides cases of mosaicisms with deletions and a case of germline mosaicism. Moreover, several of the mutations found, although occurring in distinct parts of FMR1 gene, can alter the aminoacid sequence of FMRP protein. ConclusionOur critical review presents several non-CGG repeat mutations in FMR1 gene that are directly involved in the phenotypes found in Fragile X Syndrome, indicating that genetic screening for this neurodevelopmental condition should not be restricted to the CGG repeats.

TRAF7 syndrome, a multisystemic neurodevelopmental disorder caused by germline missense variants in the TRAF7 gene, exhibits heterogeneous clinical presentations. We present a detailed description of eleven new TRAF7 syndrome cases, featuring eight distinct variants, including a novel one. Phenotypic analysis and a comprehensive review of the 58 previously reported cases outline consistent clinical presentations, emphasizing dysmorphic features, developmental delay, endocrine manifestations, and cardiac defects. In this enlarged collection, novelties include a wider range of cognitive dysfunction, with some individuals exhibiting normal development despite early psychomotor delay. Communication challenges, particularly in expressive language, are prevalent, necessitating alternative communication methods. Autistic traits, notably rigidity, are observed in the cohort. Also, worth highlighting are hearing loss, sleep disturbances, and endocrine anomalies, including growth deficiency. Cardiac defects, frequently severe, pose early-life complications. Facial features, including arched eyebrows, contribute to the distinct gestalt. A novel missense variant, p.(Arg653Leu), further underscores the complex relationship between germline TRAF7 variants and somatic changes linked to meningiomas. Our comprehensive analysis expands the phenotypic spectrum, emphasizing the need for oncological evaluations and proposing an evidence-based schedule for clinical management. This study contributes to a better understanding of TRAF7 syndrome, offering insights for improved diagnosis, intervention, and patient care. Key MessageTRAF7 syndrome, a complex neurodevelopmental disorder, exhibits variable cognitive outcomes, complex behavioral presentation and clinical complications emphasizing the need for tailored interventions and follow-up.

PurposeWhole exome or genome sequencing (WES and WGS, respectively) can be valuable in identifying the molecular basis of inherited retinal disorders (IRD), particularly when panel-based testing yields negative or inconclusive results. However, WES or WGS may reveal secondary findings (SF) associated with severe diseases such as cancer, neurodegenerative and cardiovascular conditions. The American Society of Medical Genetics and Genomics has defined a list of reportable SFs that entail significant health implications. Acknowledging the limited awareness of SFs among ophthalmologists, we sought to understand the frequency, characteristics, and impact of SF following WES/WGS. DesignRetrospective cross-sectional study Subjects, Participants and/or ControlsWe included patients with suspected IRD who underwent WES or WGS at Johns Hopkins Hospital from 2019-2024. WES/WGS was ordered following genetic counseling and consenting by certified genetic counselors (CGCs). Methods/ Main Outcome MeasuresWe conducted a qualitative analysis of WES/WGS indications and SF. We also analyzed SF consent status and recommended clinical actions. ResultsThe study included 36 patients, 50% of whom were females. 34 patients received WES, and two received WGS. The mean age was 45 {+/-} 24 years. 89% (32/36) patients consented to examine SF, while 11% declined analysis. Of the 32 patients who consented to SF analysis, 5 had SFs (16%). Detected SF included pathogenic or likely pathogenic variants in the APC, RET, TP53, MUTYH, and BRCA2 genes associated with familial adenomatous polyposis, multiple endocrine neoplasia, Li-Fraumeni syndrome, MYH-associated polyposis, and hereditary breast and ovarian cancer, respectively. After WES/WGS, patients were advised to continue managing their symptoms with their healthcare team, take further medical actions, and/or encourage family members to pursue SF genetic testing. Of the 33 individuals who received post-test genetic counseling, 79% (26/33) were counseled by a CGC, 18% (6/33) by an ophthalmologist, and 3% (1/33) by a primary care provider. IRD gene results were positive in six (16%) patients, none of whom had SF. ConclusionsSF are not infrequent when pursuing WES/WGS for diagnostic testing in IRDs. This study highlights the need for ophthalmologists to be prepared to discuss and manage SF. Multidisciplinary care, including a CGC, enables successful clinical management in this context.

IntroductionParents of children with differences of sex development (DSD) and hypospadias experience significant psychological distress, but the specific factors contributing to anxiety in these parents remain poorly understood. ObjectivesIdentify psychosocial factors associated with anxiety symptoms among parents of children with urogenital conditions and compare anxiety levels to parents in other pediatric care settings. MethodsWe conducted a cross-sectional survey study of 108 parents of children with urogenital conditions without established genetic diagnoses. Assessments included anxiety symptom scores (GAD-7), stigma measures, quality of life instruments, and demographic factors. Results were compared with 346 parents from BabySeq, a clinical trial of newborn genomic sequencing: 278 parents of healthy newborns, 68 parents of NICU infants. Backward elimination and LASSO regression modeling with multiple imputation identified key factors associated with anxiety symptoms. ResultsClinically significant anxiety (GAD-7 [&ge;]5) was present in 33% of parents of children with urogenital conditions, similar to the rate in parents of NICU infants (34%) and significantly higher than in parents of healthy newborns (21%, p=0.03). Forty-one percent of parents reported self-blame for their childs condition, while 16% blamed their partners. DSD-related quality of life decreased with increasing stigma (p=0.001), genital atypicality (p=0.03), and anxiety scores (p=0.04). Four factors consistently predicted increased anxiety across multivariate models: higher intolerance of uncertainty, increased parental health-related stress, lower educational level, and greater emotional stigma. Additional factors included greater genital atypicality, social isolation, and self-blame. DiscussionParents of children with urogenital conditions experience anxiety levels comparable to those with critically ill infants despite their children being medically stable. The identification of specific risk factors, particularly uncertainty intolerance and emotional stigma, provides targets for clinical screening and early intervention to support these families.

NAA15 is a member of the NatA N-terminal acetyltransferase complex, which also includes the NAA10 enzymatic sub-unit. Individuals with variants in the NAA15 coding region develop NAA15-related neurodevelopmental syndrome, which presents with a wide array of manifestations that affect the heart, brain, musculoskeletal system, and behavioral and cognitive development. We tracked a cohort of 27 participants (9 females and 18 males) over time, each with a pathogenic NAA15 variant, and administered the Vineland-3 assessment to assess their adaptive functioning. We found that the cohort performed significantly worse compared to the normalized Vineland values. On average, females performed better than males, and they performed significantly better on the Motor Domain and Fine Motor Sub-Domain portions of the assessment. Over time, females showed a decrease in adaptive functioning, with the decline being especially correlated at the Coping, Domestic, and Fine motor sub-domains. Males (after excluding one outlier) showed a moderate positive correlation between age and ABC standard score. Ultimately, additional longitudinal data should be collected to determine the validity of the between sex-differences and to better understand the change in adaptive behavioral outcomes of individuals with NAA15-neurodevelopmental disorder as they age.

CHAMP1 disorder is a genetic neurodevelopmental condition caused by mutations in the CHAMP1 gene that result in premature termination codons. The disorder is associated with intellectual disability, medical comorbidities, and dysmorphic features. Deletions of the CHAMP1 gene, as part of 13q3 deletion syndrome, have been briefly described with the suggestion of a milder clinical phenotype. To date, no studies have directly assessed differences between individuals with mutations in CHAMP1 to those with deletions of the gene. We completed prospective clinical evaluations of 16 individuals with mutations and eight with deletions in CHAMP1. Analyses revealed significantly lower adaptive functioning across all domains assessed (i.e., communication, daily living skills, socialization, and motor skills) in the mutation group. Developmental milestones and medical features further showed difference between groups. The phenotypes associated with mutations, as compared to deletions, indicate likely difference in pathogenesis between groups, where deletions are acting through CHAMP1 haploinsufficiency and mutations are acting through dominant negative or gain of function mechanisms, leading to a more severe clinical phenotype. Understanding this pathogenesis is important to the future of novel therapies for CHAMP1 disorder and illustrates that mechanistic understanding of mutations must be carefully considered prior to treatment development.

BackgroundThe underlying cause of central nervous system (CNS) tumors in children is largely unknown. In this nationwide, prospective population-based study we investigate rare germline variants across known and putative CPS genes and genes exhibiting evolutionary intolerance of inactivating alterations in children with CNS tumors. MethodsOne hundred and twenty-eight children with CNS tumors underwent whole-genome sequencing of germline DNA. Single nucleotide and structural variants in 315 cancer related genes and 2,986 highly evolutionarily constrained genes were assessed. A systematic pedigree analysis covering 3,543 close relatives was performed. ResultsThirteen patients harbored rare pathogenic variants in nine known CPS genes. The likelihood of carrying pathogenic variants in CPS genes was higher for patients with medulloblastoma than children with other tumors (OR 5.9, CI 1.6-21.2). Metasynchronous CNS tumors were observed exclusively in children harboring pathogenic CPS gene variants (n=2, p=0.01). In general, known pCPS genes were shown to be significantly more constrained than both genes associated with risk of adult-onset malignancies (p=5e-4) and all other genes (p=5e-17). Forty-seven patients carried 66 loss-of-functions variants in 60 constrained genes, including eight variants in six known pCPS genes. A deletion in the extremely constrained EHMT1 gene, formerly somatically linked with sonic hedgehog medulloblastoma, was found in a patient with this tumor. Conclusions{bsim}10% of pediatric CNS tumors can be attributed to rare variants in known CPS genes. Analysis of evolutionarily constrained genes may increase our understanding of pediatric cancer susceptibility. 3 key pointsO_LI{bsim}10% of children with CNS tumors carry a pathogenic variant in a known cancer predisposition gene C_LIO_LIKnown pediatric-onset cancer predisposition genes show high evolutionary constraint C_LIO_LILoss-of-function variants in evolutionarily constrained genes may explain additional risk C_LI Importance of this studyAlthough CNS tumors constitute the most common form of solid neoplasms in childhood, our understanding of their underlying causes remains sparse. Predisposition studies often suffer from selection bias, lack of family and clinical data or from being limited to SNVs in established cancer predisposition genes. We report the findings of a prospective, population-based investigation of genetic predisposition to pediatric CNS tumors. Our findings illustrate that 10% of children with CNS tumors harbor a damaging alteration in a known cancer gene, of which the majority (9/13) are loss-of-function alterations. Moreover, we illustrate how recently developed knowledge on evolutionarily loss-of-function intolerant genes may be used to investigate additional pediatric cancer risk and present EHMT1 as a putative novel predisposition gene for SHH medulloblastoma. Previously undescribed links between variants in known cancer predisposition genes and specific brain tumors are presented and the importance of assessing both SV and SNV is illustrated.